The compound eye in the opaque-eye phenotype ofDrosophila melanogaster

The compound eye of the opaque-eye mutant ofDrosophila melanogaster was investigated by means of electron microscopy to determine the morphological and physical properties of ommatidial elements. These elements in the mutant were found to differ from those of the wild-type flies in the following ways: (1) The cuticular lens was thinner than that of the control and lacked the typical lamellar construction. (2) The Semper cells were irregular in shape and contained many membranous inclusions similar to those found in degenerating cells; also their nuclei contained virus-like particles. (3) The primary pigment cells contained an abundance of drosopterin-containing granules which were lacking in those of wild-type flies. (4) The superior and inferior central photoreceptor cells were misplaced and their rhabdomeres evidenced some degeneration. (5) The secondary pigment cells had only one type of pigment granules instead of the three types found in the control. These morphological changes in ommatidial elements induced physical abnormalities such as the apparent opaqueness of the eye, the lack of a pseudopupil, the probable disability of the photoreceptor cells to respond to light and the inability of the dioptric system to produce utilizable geometrical images.     

Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma

Somatic sequencing of cancers has produced new insight into tumorigenesis, tumor heterogeneity, and disease progression, but the vast majority of genetic events identified are of indeterminate clinical significance. Here, we describe a NextGen sequencing approach to fully analyzing 248 genes, including all those of known clinical significance in melanoma. This strategy features solution capture of DNA followed by multiplexed, high‐throughput sequencing and was evaluated in 31 melanoma cell lines and 18 tumor tissues from patients with metastatic melanoma. Mutations in melanoma cell lines correlated with their sensitivity to corresponding small molecule inhibitors, confirming, for example, lapatinib sensitivity in ERBB4 mutant lines and identifying a novel activating mutation of BRAF. The latter event would not have been identified by clinical sequencing and was associated with responsiveness to a BRAF kinase inhibitor. This approach identified focal copy number changes of PTEN not found by standard methods, such as comparative genomic hybridization (CGH). Actionable mutations were found in 89% of the tumor tissues analyzed, 56% of which would not be identified by standard‐of‐care approaches. This work shows that targeted sequencing is an attractive approach for clinical use in melanoma.     

Enrichment of ANME‐2 dominated anaerobic methanotrophy from cold seep sediment in an external ultrafiltration membrane bioreactor

Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is a microbially mediated unique natural phenomenon with an ecological relevance in the global carbon balance and potential application in biotechnology. This study aimed to enrich an AOM performing microbial community with the main focus on anaerobic methanotrophic archaea (ANME) present in sediments from the Ginsburg mud volcano (Gulf of Cadiz), a known site for AOM, in a membrane bioreactor (MBR) for 726 days at 22 (± 3)°C and at ambient pressure. The MBR was equipped with a cylindrical external ultrafiltration membrane, fed a defined medium containing artificial seawater and operated at a cross flow velocity of 0.02 m/min. Sulfide production with simultaneous sulfate reduction was in equimolar ratio between days 480 and 585 of MBR operation, whereas methane consumption was in oscillating trend. At the end of the MBR operation (day 726), the enriched biomass was incubated with ¹³C labeled methane, ¹³C labeled inorganic carbon was produced and the AOM rate based on ¹³C‐inorganic carbon was 1.2 μmol/(g_dw d). Microbial analysis of the enriched biomass at 400 and 726 days of MBR operation showed that ANME‐2 and Desulfosarcina type sulfate reducing bacteria were enriched in the MBR, which formed closely associated aggregates. The major relevance of this study is the enrichment of an AOM consortium in a MBR system which can assist to explore the ecophysiology of ANME and provides an opportunity to explore the potential application of AOM.     

BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank

Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of `Magnetic Resonance' (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu).     

<Emphasis Type="Italic">snail</Emphasis> expression during embryonic development of the coral<Emphasis Type="Italic"> Acropora</Emphasis>: blurring the diploblast/triploblast divide?

Although corals are nominally diploblastic, the early development of Acropora millepora involves a process that clearly resembles gastrulation in higher metazoans. This similarity at the morphological level led us to search for the Acropora equivalents of genes whose key roles in gastrulation are conserved across the higher Metazoa. We here report the characterisation of one such gene, snail, which in both Drosophila and the mouse is expressed in cells undergoing an epithelial-mesenchyme transition and/or morphogenetic movements. In addition to an N-terminal SNAG domain, the Acropora snail protein contains four zinc fingers with sequences diagnostic for members of the snail protein subfamily. In situ hybridisation reveals expression in epithelial tissue in the central portion of one side of the flattened pre-gastrulation embryo, which continues to express snail as it is engulfed by its opposite layer. Comparison to snail expression during gastrulation in bilaterians such as Drosophila reveals striking similarities and suggests mechanistic, and possibly evolutionary, links between the processes of mesoderm formation in bilaterians and endoderm formation in the Cnidaria.Edited by P. Simpson     

Oligogenic combinations associated with breast cancer risk in women under 53 years of age

Common, but weakly penetrant, functional polymorphisms probably account for most of the genetic risk for breast cancer in the general population. Current polygenic risk models assume that component genes act independently. To test for potential gene-gene interactions, single nucleotide polymorphisms in ten genes with known or predicted roles in breast carcinogenesis were examined in a case-control study of 631 Caucasian women diagnosed with breast cancer under the age of 53 years and 1,504 controls under the age of 53 years. Association of breast cancer risk with individual genes and with two- and three-gene combinations was analyzed. Sixty-nine oligogenotypes from 37 distinct two- and three-gene combinations met stringent criteria for significance. Significant odds ratios (ORs) covered a 12-fold range: 0.5-5.9. Of the observed ORs, 17% differed significantly from the ORs predicted by a model of independent gene action, suggesting epistasis, i.e., that these genes interact to affect breast cancer risk in a manner not predictable from single gene effects. Exploration of the biological basis for these oligogenic interactions might reveal etiologic or therapeutic insights into breast cancer and other cancers.     

Tandem organization of independently duplicated homeobox genes in the basal cnidarian <Emphasis Type="Italic">Acropora millepora</Emphasis>

A number of examples of independently duplicated regulatory genes have been identified in cnidarians, but the extent of this phenomenon and organization of these duplicated genes are unknown. Here we describe the identification of three pairs of independently duplicated homeobox genes in the anthozoan cnidarian, Acropora millepora. In each case, the pairs of paralogous genes are tightly linked, but the extent of sequence divergence implies that these do not reflect recent duplication events. The phenomenon is likely to be more general, as the examples reported here represent most of the limited number of Acropora homeobox genes for which genomic data are yet available.N. Hislop and D. de Jong contributed equally to this workEdited by M. Akam     

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user- and software-dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure-based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord.     

Biotreatment of a gas-phase volatile mixture from fibreglass and composite manufacturing industries

Acetone, toluene and styrene (ATS) are representative air pollutants emanating during the production process in fibreglass and composite manufacturing industries. In this study, the performance of a steady-state biofilter inoculated with the fungus Sporothrix variecibatus was tested at different empty bed residence times (EBRTs), and at different inlet concentrations of ATS, corresponding to total pollutant loading rates ranging from 30 to 490 gm(-3)hour(-1). Styrene was somewhat better removed (47-100%) in the biofilter than acetone (34-100%) and toluene (42-100%), with maximum elimination capacities (EC(max)) of 108, 72 and 144 gm(-3)hour(-1), for ATS, respectively. Besides, it was observed that, although increasing the concentration of ATS decreased their removal, the presence of toluene also decreased the EC(max) of both acetone and toluene in the ternary mixture. During transient operations, the biofilter was subjected to intermittent shutdown and re-start operations where the gas-phase pollutant flow was stopped for either 5 or 16d. It was observed that, for longer shutdown periods (16d), the biofilter required nearly 8-10d to reach similar removal patterns to those observed before the shutdown phase. Batch biodegradation tests were conducted, using Sporothrix-like microorganisms present in the leachate of the biofilter, with a mixture of ATS as the sole carbon source. Complete removal of ATS was observed within the test period of 168 hours. Styrene was degraded faster, with a specific substrate utilization rate of 0.9 mg styrenemg biomass(-1)hour(-1), followed by toluene (0.6) and acetone (0.44). The effectiveness of the biofilter to reach high total EC (321.3 gm(-3)hour(-1)), and withstand transient operations shows the robustness of this fungal-bioreactor and its suitability to handle emissions from a fibreglass and composite manufacturing industry.